# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 18:09:43 2020
#   Inital geometry file: a 52 line input string
#   Ligand name: [(1R)-1-amino-2-methylpropyl]phosphonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)[C@H](N)[P](O)(O)=O
#
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
_chem_comp.initial_date
_chem_comp.modified_date
_chem_comp.source
 PVA  PVA  '[(1R)-1-amino-2-methylpropyl]phosphonic acid'  ligand  19  9  .  2021-08-20  2021-08-20  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_PVA
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.charge
_chem_comp_atom.partial_charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
 PVA  C1   C  CH1    0  -0.323  -0.5747   0.7437   0.4606
 PVA  C2   C  CH1    0  -0.218   0.0461   0.2728   1.7892
 PVA  C3   C  CH3    0  -0.647  -0.0620  -1.2315   2.0215
 PVA  CM   C  CH3    0  -0.662   1.4861   0.7423   1.9663
 PVA  N    N  NH2    0  -0.816  -2.0378   0.6928   0.4790
 PVA  P    P  P      0   1.178  -0.0189  -0.1439  -1.1049
 PVA  O1P  O  O      0  -0.909  -0.8746  -1.4231  -1.1382
 PVA  O2P  O  OP    -1  -0.915  -0.3489   0.8325  -2.2442
 PVA  O3P  O  OP    -1  -0.890   1.4876  -0.4133  -0.9714
 PVA  H1   H  HCH1   0   0.163  -0.2825   1.7985   0.3486
 PVA  H2   H  HCH1   0   0.175  -0.5392   0.7619   2.5841
 PVA  H31  H  HCH3   0   0.196   0.2336  -1.4860   3.0419
 PVA  H32  H  HCH3   0   0.203  -1.0807  -1.5926   1.8716
 PVA  H33  H  HCH3   0   0.211   0.5851  -1.7755   1.3347
 PVA  HM1  H  HCH3   0   0.227   2.1275   0.2771   1.2204
 PVA  HM2  H  HCH3   0   0.199   1.5659   1.8262   1.8463
 PVA  HM3  H  HCH3   0   0.197   1.8645   0.4950   2.9614
 PVA  HN1  H  HNH2   0   0.321  -2.3121  -0.2680   0.3120
 PVA  HN2  H  HNH2   0   0.311  -2.3832   0.9344   1.4024

loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.type
_chem_comp_bond.value_dist
_chem_comp_bond.value_dist_esd
_chem_comp_bond.value_dist_neutron
 PVA  C1  C2   single  1.540  0.020  1.540
 PVA  C1  N    single  1.464  0.020  1.464
 PVA  C1  P    single  1.883  0.020  1.883
 PVA  C1  H1   single  0.970  0.020  1.090
 PVA  C2  C3   single  1.526  0.020  1.526
 PVA  C2  CM   single  1.525  0.020  1.525
 PVA  C2  H2   single  0.970  0.020  1.090
 PVA  C3  H31  single  0.970  0.020  1.090
 PVA  C3  H32  single  0.970  0.020  1.090
 PVA  C3  H33  single  0.970  0.020  1.090
 PVA  CM  HM1  single  0.970  0.020  1.090
 PVA  CM  HM2  single  0.970  0.020  1.090
 PVA  CM  HM3  single  0.970  0.020  1.090
 PVA  N   HN1  single  0.890  0.020  1.040
 PVA  N   HN2  single  0.890  0.020  1.040
 PVA  P   O1P  deloc   1.539  0.020  1.539
 PVA  P   O2P  deloc   1.536  0.020  1.536
 PVA  P   O3P  deloc   1.536  0.020  1.536

loop_
_chem_comp_angle.comp_id
_chem_comp_angle.atom_id_1
_chem_comp_angle.atom_id_2
_chem_comp_angle.atom_id_3
_chem_comp_angle.value_angle
_chem_comp_angle.value_angle_esd
 PVA  H1   C1  P    106.78  3.000
 PVA  H1   C1  N    107.46  3.000
 PVA  P    C1  N    106.79  3.000
 PVA  H1   C1  C2   105.90  3.000
 PVA  P    C1  C2   117.00  3.000
 PVA  N    C1  C2   112.42  3.000
 PVA  H2   C2  CM   106.33  3.000
 PVA  H2   C2  C3   106.87  3.000
 PVA  CM   C2  C3   110.65  3.000
 PVA  H2   C2  C1   105.82  3.000
 PVA  CM   C2  C1   112.75  3.000
 PVA  C3   C2  C1   113.84  3.000
 PVA  H33  C3  H32  107.62  3.000
 PVA  H33  C3  H31  108.17  3.000
 PVA  H32  C3  H31  107.68  3.000
 PVA  H33  C3  C2   110.75  3.000
 PVA  H32  C3  C2   111.80  3.000
 PVA  H31  C3  C2   110.66  3.000
 PVA  HM3  CM  HM2  107.39  3.000
 PVA  HM3  CM  HM1  108.87  3.000
 PVA  HM2  CM  HM1  107.79  3.000
 PVA  HM3  CM  C2   111.29  3.000
 PVA  HM2  CM  C2   111.18  3.000
 PVA  HM1  CM  C2   110.21  3.000
 PVA  HN2  N   HN1  106.47  3.000
 PVA  HN2  N   C1   110.07  3.000
 PVA  HN1  N   C1   107.55  3.000
 PVA  O3P  P   O2P  112.74  3.000
 PVA  O3P  P   O1P  113.65  3.000
 PVA  O2P  P   O1P  113.12  3.000
 PVA  O3P  P   C1   107.44  3.000
 PVA  O2P  P   C1   104.69  3.000
 PVA  O1P  P   C1   104.21  3.000

loop_
_chem_comp_tor.comp_id
_chem_comp_tor.id
_chem_comp_tor.atom_id_1
_chem_comp_tor.atom_id_2
_chem_comp_tor.atom_id_3
_chem_comp_tor.atom_id_4
_chem_comp_tor.value_angle
_chem_comp_tor.value_angle_esd
_chem_comp_tor.period
 PVA  Var_01  H31  C3  C2  C1  -170.22  30.0  3
 PVA  Var_02  HM1  CM  C2  C1   -65.67  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 PVA  chir_01  C1  C2  N  P  positiv

